Microorganisms play a variety of important roles in human biology. They synthesize vitamins, inhibit pathogens, modulate fat storage and the immune system, and cause cancers and infectious diseases. Despite these important findings, our overall understanding of the microbial role in human biology is still in its infancy. Slow progress in this area is caused by limitations of the currently used methods for studying microbial communities, including insufficient throughput and high cost. The Specific Aims of this proposal address these limitations through the development of new high- throughput methods and software. In particular, we will develop (1) a high-throughput, rRNA gene based method to identify microorganisms, (2) novel approaches to characterize the associations between levels of specific microorganisms and health or disease processes, and (3) an integrated software suite to support and automate these experimental processes. Specific Aim (4) is to perform comprehensive tests to validate our methods and evaluate their utility in comparison to other approaches. These new experimental capabilities will enable us to address the long-term objective of our research, which is to understand the role of microorganisms in the etiology of inflammatory bowel disease (IBD) and in the development and homeostasis of mucosal immunity in humans. They will also enable a myriad of investigations aimed at identifying microorganisms involved in other human health and disease processes. This project addresses the mission of the NIH Roadmap and the PA "Innovations in Biomedical Computational Science and Technology" by utilizing an interdisciplinary research team to develop innovative molecular, computational, and statistical methods for studying the roles of microorganisms in human health and disease processes. The results of our work are likely to impact areas outside of microbiology, as the proposed methods and software could prove useful in microarray data analysis, fingerprint-based taxonomic studies, and other fields of research. PUBLIC HEALTH RELEVANCE: We propose to develop new experimental approaches to investigate the role of microorganisms in mucosal immunity, IBD and other human health and disease processes. These new tools should lead to new strategies to prevent, manage or cure IBD, as well as the multitude of other diseases associated with microorganisms.